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Table 3 Association results of the thirteen indels in eight genes on the five milk production traits (least squares mean ± SE)

From: Determination of genetic associations between indels in 11 candidate genes and milk composition traits in Chinese Holstein population

Locus Gene Genotype (No.) MY FY FP PY PP
rs381714237 FCGR2B del/del(86) 10,891 ± 99.80 385.05 ± 4.21 3.59 ± 0.040 319.32 ± 3.10ab 2.95 ± 0.014a
ins/del(380) 10,702 ± 64.80 383.94 ± 2.89 3.66 ± 0.027 315.86 ± 2.11Aa 2.98 ± 0.009ab
ins/ins(282) 10,834 ± 68.20 385.61 ± 3.03 3.64 ± 0.028 321.83 ± 2.20Bb 2.99 ± 0.009b
P value 0.0297* 0.7926 0.1738 0.0041** 0.0198*
ss2137349053 CENPE del/del(153) 10,403 ± 55.66A 374.36 ± 2.82Aa 3.61 ± 0.034 308.40 ± 2.65A 2.97 ± 0.024
del/ins(373) 10,661 ± 47.88B 378.61 ± 2.43Aa 3.57 ± 0.027 315.70 ± 2.14Ba 2.97 ± 0.017
ins/ins(209) 10,852 ± 51.03C 385.99 ± 2.59B 3.58 ± 0.031 321.05 ± 2.37Bb 2.97 ± 0.020
P value < 0.0001** < 0.0001** 0.3733 < 0.0001** 0.9882
rs385060942 CENPE del/del(152) 10,494 ± 84.00Aa 376.49 ± 3.60Aa 3.60 ± 0.034 310.45 ± 2.62B 2.96 ± 0.012
del/ins(377) 10,717 ± 65.77Aa 381.44 ± 2.93ab 3.57 ± 0.027 318.18 ± 2.13Aa 2.97 ± 0.009
ins/ins(208) 10,871 ± 74.83B 387.82 ± 3.26Bb 3.59 ± 0.031 322.24 ± 2.38Aa 2.97 ± 0.010
P value < 0.0001** 0.0045** 0.6063 < 0.0001** 0.6166
ss2137349051 CENPE ins/ins(206) 10,817 ± 75.26A 386.81 ± 3.28A 3.60 ± 0.031 321.11 ± 2.39A 2.97 ± 0.010
del/ins(382) 10,586 ± 65.52Ba 378.41 ± 2.92Ba 3.59 ± 0.027 314.42 ± 2.12Ba 2.98 ± 0.009
del/del(156) 10,397 ± 83.94Bb 374.49 ± 3.61Ba 3.61 ± 0.034 308.61 ± 2.63Bb 2.97 ± 0.012
P value < 0.0001** 0.0010** 0.7289 < 0.0001** 0.9571
rs453960300 CENPE ins/ins(158) 10,380 ± 83.33Aa 375.15 ± 3.58 3.63 ± 0.034 307.63 ± 2.61Aa 2.98 ± 0.012
ins/del(381) 10,586 ± 66.10b 380 ± 2.95 3.61 ± 0.027 313.34 ± 2.15b 2.98 ± 0.009
del/del(207) 10,764 ± 74.83Bc 385.96 ± 3.26 3.61 ± 0.031 318.18 ± 2.38Bc 2.97 ± 0.010
P value < 0.0001** 0.0073** 0.7589 0.0002** 0.9461
rs378415122 CENPE ins/ins(158) 10,373 ± 83.79Aa 373.03 ± 3.60Aa 3.62 ± 0.034 306.81 ± 2.62Aa 2.97 ± 0.012
ins/del(386) 10,547 ± 65.79Aa 377.75 ± 2.93a 3.60 ± 0.027 312.15 ± 2.13Aa 2.97 ± 0.009
del/del(207) 10,785 ± 74.23B 386.21 ± 3.23Bb 3.60 ± 0.030 319.19 ± 2.36B 2.97 ± 0.010
P value < 0.0001** 0.0004** 0.8913 < 0.0001** 0.9535
rs134985825 RETSAT del/del(205) 10,774 ± 75.77Aa 383.94 ± 3.30ab 3.58 ± 0.031 318.23 ± 2.40ab 2.96 ± 0.010a
del/ins(370) 10,563 ± 66.51B 378.10 ± 2.95Aa 3.60 ± 0.027 314.44 ± 2.15Aa 2.98 ± 0.009ab
ins/ins(169) 10,823 ± 79.45Aa 388.92 ± 3.43Bb 3.61 ± 0.032 323.7 ± 2.50Bb 2.99 ± 0.011b
P value 0.0003** 0.0009** 0.6500 0.0001** 0.0237*
rs377943075 ACSBG2 del/del(62) 10,746 ± 111.22 378.40 ± 4.68Aa 3.56 ± 0.045 318.61 ± 3.42 3.00 ± 0.016ab
del/ins(294) 10,776 ± 69.04 387.18 ± 3.03ab 3.61 ± 0.028 319.22 ± 2.19 2.99 ± 0.009Ab
ins/ins(401) 10,884 ± 63.81 391.00 ± 2.84Bb 3.62 ± 0.026 319.31 ± 2.05 2.97 ± 0.008Ba
P value 0.1334 0.0088** 0.4393 0.9749 0.0052**
rs136639319 TBC1D1 ins/ins(19) 10,752 ± 182.68 391.92 ± 7.47 3.65 ± 0.073ab 320.14 ± 5.45 2.98 ± 0.026ab
del/ins(242) 10,564 ± 72.44 383.75 ± 3.18 3.65 ± 0.030a 314.38 ± 2.32 2.99 ± 0.010a
del/del(493) 10,659 ± 64.49 380.06 ± 2.88 3.58 ± 0.027b 314.42 ± 2.1 2.96 ± 0.009b
P value 0.2493 0.1198 0.0224* 0.5384 0.0209*
rs379188781 NLK ins/ins(277) 10,676 ± 70.45 377.09 ± 3.11 3.56 ± 0.029 318.23 ± 2.26 2.99 ± 0.009Aa
del/ins(347) 10,627 ± 67.41 381.09 ± 3.00 3.60 ± 0.028 314.48 ± 2.18 2.97 ± 0.009b
del/del(117) 10,749 ± 90.28 384.24 ± 3.83 3.57 ± 0.037 315.92 ± 2.79 2.95 ± 0.013Bb
P value 0.3389 0.1020 0.2615 0.1279 0.0047**
rs134444531 NLK ins/ins(197) 10,748 ± 78.14 384.18 ± 3.40 3.58 ± 0.032 322.04 ± 2.47Aa 2.99 ± 0.011a
del/ins(395) 10,723 ± 65.31 386.23 ± 2.91 3.61 ± 0.027 317.93 ± 2.12a 2.97 ± 0.009ab
del/del(150) 10,563 ± 85.88 381.58 ± 3.68 3.63 ± 0.035 312.32 ± 2.68Bb 2.96 ± 0.012b
P value 0.0733 0.3026 0.4078 0.0012** 0.0257*
ss2137349058 MAP3K1 ins/ins(152) 10,482 ± 82.27Aa 372.63 ± 3.54Aa 3.58 ± 0.034 310.01 ± 2.58Aa 2.97 ± 0.011
del/ins(380) 10,613 ± 66.30Aa 376.47 ± 2.94Aa 3.56 ± 0.027 314.12 ± 2.14Aa 2.97 ± 0.009
del/del(202) 10,909 ± 77.27Bb 390.47 ± 3.35Bb 3.59 ± 0.032 323.13 ± 2.44Bb 2.97 ± 0.011
P value < 0.0001** < 0.0001** 0.4863 < 0.0001** 0.8495
ss2019489562 UGDH del/del(405) 10,860 ± 64.35a 387.55 ± 2.89 3.64 ± 0.027 318.31 ± 2.11 2.99 ± 0.009
del/ins(4) 9902 ± 384.75b 376.58 ± 15.49 3.81 ± 0.153 299.74 ± 11.30 3.02 ± 0.056
ins/ins(342) 10,798 ± 66.31ab 388.28 ± 2.95 3.64 ± 0.027 315.05 ± 2.13 2.97 ± 0.009
P value 0.0312* 0.7267 0.5077 0.0532 0.0567
  1. Note:*significant association at the significance level of 0.05; **significant association at the significance level of 0.01
  2. The different superscripts (A,B within the same column with different superscripts indicate P < 0.01; a,b indicate P < 0.05) adjusted after correction for multiple testing indicate significant differences among the genotypes
  3. MY milk yield, FY fat yield, FP fat percentage, PY protein yield, PP protein percentage